Frequently Asked Questions

How do I obtain individual-level data?
Each project has its own information on how and where individual-level data can be obtained. Please see the Project Description tab for specifics on data for that project.

How do I cite data from this site?
See the Data Usage page for detailed citation instructions and guidelines.

Where is the X-chromosome in the Genes and Interactions Controlling Oral Clefts data?
The data for this project is limited to autosomes.

Why is there no Manhattan Plot for the options I selected?
If the data has an insufficient sample size (e.g., number of trios) for the analysis, no plot will be displayed.

Why is my Custom Region plot taking so long?
Locus Zoom is utlilized to generate the custom plots. The software needs time to read in the files - which can be quite large, especially for imputed data - and to create the plots. This process can sometimes take upwards of 5-10 minutes.

Why is my LocusZoom plot colored grey?
In LocusZoom plots, the data points are colored according to their level of linkage disequilibrium (LD) of each SNP with the index SNP. If a SNP is specified, LD of all data points will be relative to the user-specified index SNP. If the region or gene is specified, LocusZoom automatically selects the most significant SNP in the region as the index SNP. For all other SNPs in the plot, the color of the data point will reflect the pairwise LD with this index SNP. The default LD measure is r2 calculated from 1000 Genomes. SNPs with missing LD information are shown in grey.

Why am I getting a LocusZoom error?
A plot may not be generated if the SNP name or gene name cannot be found. Please double-check the gene name exists in the UCSC browser before requesting a plot based on gene name. If you have queried the database by SNP or Gene, try to put in the coordinates of the region you are interested. In some cases, you will continue to get an error if the queried region simply has no data points to plot.

Alternatively, please check the error message returned when a plot cannot be generated. If the error indicates a missing file, we have removed these results from the database for insufficient samples sizes in the analysis.

If your error happens after you searched for chromosome base pairs, it is possibly due to formatting. The input needs to be: chr#:bp-bp (example - 4:4412292−5416561). The software is sensitive and there is no flexibility in format.

Should you receive an error, please copy and paste it into an email to our help desk. Seeing the error text can help us troubleshoot and fix the problem.

Help!
If you are having any other problems, questions, or concerns, please contact our Help Desk.